SMTL ID : 6pfz.2 (1 other biounit)

Structure of a NAD-Dependent Persulfide Reductase from A. fulgidus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 29 residues within 4Å: Chain A: I.6, G.7, G.8, G.9, A.10, A.11, V.31, E.32, A.33, R.41, C.42, P.45, T.84, V.85, A.86, A.115, T.116, G.117, L.136, I.164, G.286, D.287, P.303, F.304, G.305, D.306, A.308 Chain B: Y.430, P.432 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.136, A:I.164, A:I.164 Hydrogen bonds: A:G.8, A:A.10, A:A.11, A:G.12, A:A.33, A:R.41, A:A.86, A:A.86, A:D.287, A:D.287, A:D.287, A:P.303, A:G.305, A:D.306, B:Y.430 Salt bridges: A:R.41 pi-Stacking: A:F.163 FAD.4: 31 residues within 4Å: Chain A: Y.430, A.431, P.432 Chain B: I.6, G.7, G.8, G.9, A.10, A.11, V.31, E.32, A.33, R.41, C.42, P.45, T.84, V.85, A.86, A.115, T.116, G.117, L.136, F.163, I.164, G.286, D.287, P.303, F.304, G.305, D.306, A.308 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.164 Hydrogen bonds: B:G.8, B:A.10, B:A.11, B:A.33, B:R.41, B:A.86, B:A.86, B:D.287, B:P.303, B:G.305, B:D.306, A:Y.430 Salt bridges: B:R.41 pi-Stacking: B:F.163, B:F.163

2 x COA: COENZYME A(Non-covalent)

COA.2: 24 residues within 4Å: Chain A: A.10, K.14, S.17, R.18, R.21, S.38, G.40, C.42, F.72, K.76, N.309, R.313 Chain B: A.364, P.365, Y.372, Y.430, T.443, N.446, V.447, N.450, I.521, G.522, L.523, F.526 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.72 Hydrogen bonds: A:S.17, A:N.309, B:N.450, B:I.521 Salt bridges: A:K.14, A:K.14, A:K.14, A:R.18, A:R.21, A:R.21, A:R.21, A:K.76, A:R.313 COA.5: 26 residues within 4Å: Chain A: A.364, P.365, Y.372, Y.430, T.443, V.447, N.450, I.521, G.522, L.523, F.526 Chain B: G.9, A.10, K.14, S.17, R.18, R.21, S.38, L.39, G.40, C.42, R.67, F.72, K.76, N.309, R.313 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.72 Hydrogen bonds: B:S.17, B:R.21, A:T.443, A:N.450, A:I.521 Salt bridges: B:K.14, B:K.14, B:R.18, B:R.21, B:R.21, B:K.76, B:R.313

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.306, T.332 Chain B: D.427, L.428 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.306, A:T.332, B:D.427, B:L.428 CA.6: 4 residues within 4Å: Chain A: D.427, L.428 Chain B: D.306, T.332 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.306, B:T.332, A:D.427, A:L.428

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shabdar, S. et al., Structural and Kinetic Characterization of Hyperthermophilic NADH-Dependent Persulfide Reductase from Archaeoglobus fulgidus . Archaea (2021)

Release Date

2020-07-01

Peptides

NADH oxidase (NoxA-3): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NADH oxidase (NoxA-3)

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